I have finally solved this problem, after months of cheating and using File::Glob to do the hard work for me. (I ran into string-length limitations with File::Glob which prevented it from working for very long boolean statements.)

Here is my Perl solution, translated from (obligatory shudder) PHP. Hopefully the code speaks for itself and is not in need of much documentation for explaining its logic. NOTE: "not" nodes are skipped, because the point of this function is to come up with lists of terms that will match the logic.

#!/usr/bin/perl -l

use strict;
use warnings;

my $tree = ['and', ['or', 1, 2], ['not', 3], ['or', 4, 5, 6]];
my $opts = options($tree);

for my $o (@$opts) {
  print "OPTION: ", join(", ", @$o);
}


sub options {
  my ($tree, $opts) = @_;

  if (! $opts) {
    $opts = [ [] ];
    options($tree, $opts);
    return $opts;
  }

  else {
    my $op = $tree->[0];

    if ($op eq 'and') {
      for my $val (@$tree[1 .. $#$tree]) {
        if (ref($val) eq 'ARRAY' and ($val->[0] eq 'and' or $val->[0] 
+eq 'or' or $val->[0] eq 'not')) {
          my $subtree = options($val);
          my @new;

          for my $branch (@$subtree) {
            for my $o (@$opts) {
              push @new, [ @$o, @$branch ];
            }
          }

          @$opts = @new;
        }

        else {
          for my $o (@$opts) {
            push @$o, $val;
          }
        }
      }
    }

    elsif ($op eq 'or') {
      my @new;

      for my $val (@$tree[1 .. $#$tree]) {
        if (ref($val) eq 'ARRAY' and ($val->[0] eq 'and' or $val->[0] 
+eq 'or' or $val->[0] eq 'not')) {
          my $subtree = options($val);

          for my $branch (@$subtree) {
            for my $o (@$opts) {
              push @new, [@$o, @$branch];
            }
          }
        }

        else {
          for my $o (@$opts) {
            push @new, [@$o, $val];
          }
        }
      }

      @$opts = @new;
    }
  }
}
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